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Hudson D, Lubbock A, Basham M, Koohy H. A comparison of clustering models for inference of T cell receptor antigen specificity. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024; 13:None. [PMID: 38525047 PMCID: PMC10955519 DOI: 10.1016/j.immuno.2024.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 03/26/2024]
Abstract
The vast potential sequence diversity of TCRs and their ligands has presented an historic barrier to computational prediction of TCR epitope specificity, a holy grail of quantitative immunology. One common approach is to cluster sequences together, on the assumption that similar receptors bind similar epitopes. Here, we provide the first independent evaluation of widely used clustering algorithms for TCR specificity inference, observing some variability in predictive performance between models, and marked differences in scalability. Despite these differences, we find that different algorithms produce clusters with high degrees of similarity for receptors recognising the same epitope. Our analysis strengthens the case for use of clustering models to identify signals of common specificity from large repertoires, whilst highlighting scope for improvement of complex models over simple comparators.
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Affiliation(s)
- Dan Hudson
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Didcot, UK
| | | | | | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Alan Turning Fellow in Health and Medicine, UK
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2
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Hawiger D. Emerging T cell immunoregulatory mechanisms in multiple sclerosis and Alzheimer's disease. Front Aging Neurosci 2024; 16:1350240. [PMID: 38435400 PMCID: PMC10904586 DOI: 10.3389/fnagi.2024.1350240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
Multiple sclerosis (MS) and Alzheimer's disease (AD) are neuroinflammatory and neurodegenerative diseases with considerable socioeconomic impacts but without definitive treatments. AD and MS have multifactorial pathogenesis resulting in complex cognitive and neurologic symptoms and growing evidence also indicates key functions of specific immune cells. Whereas relevant processes dependent on T cells have been elucidated in both AD and MS, mechanisms that can control such immune responses still remain elusive. Here, a brief overview of select recent findings clarifying immunomodulatory mechanisms specifically induced by tolerogenic dendritic cells to limit the activation and functions of neurodegenerative T cells is presented. These insights could become a foundation for new cutting-edge research as well as therapeutic strategies.
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Affiliation(s)
- Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
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3
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Britanova OV, Lupyr KR, Staroverov DB, Shagina IA, Aleksandrov AA, Ustyugov YY, Somov DV, Klimenko A, Shostak NA, Zvyagin IV, Stepanov AV, Merzlyak EM, Davydov AN, Izraelson M, Egorov ES, Bogdanova EA, Vladimirova AK, Iakovlev PA, Fedorenko DA, Ivanov RA, Skvortsova VI, Lukyanov S, Chudakov DM. Targeted depletion of TRBV9 + T cells as immunotherapy in a patient with ankylosing spondylitis. Nat Med 2023; 29:2731-2736. [PMID: 37872223 PMCID: PMC10667094 DOI: 10.1038/s41591-023-02613-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023]
Abstract
Autoimmunity is intrinsically driven by memory T and B cell clones inappropriately targeted at self-antigens. Selective depletion or suppression of self-reactive T cells remains a holy grail of autoimmune therapy, but disease-associated T cell receptors (TCRs) and cognate antigenic epitopes remained elusive. A TRBV9-containing CD8+ TCR motif was recently associated with the pathogenesis of ankylosing spondylitis, psoriatic arthritis and acute anterior uveitis, and cognate HLA-B*27-presented epitopes were identified. Following successful testing in nonhuman primate models, here we report human TRBV9+ T cell elimination in ankylosing spondylitis. The patient achieved remission within 3 months and ceased anti-TNF therapy after 5 years of continuous use. Complete remission has now persisted for 4 years, with three doses of anti-TRBV9 administered per year. We also observed a profound improvement in spinal mobility metrics and the Bath Ankylosing Spondylitis Metrology Index (BASMI). This represents a possibly curative therapy of an autoimmune disease via selective depletion of a TRBV-defined group of T cells. The anti-TRBV9 therapy could potentially be applicable to other HLA-B*27-associated spondyloarthropathies. Such targeted elimination of the underlying cause of the disease without systemic immunosuppression could offer a new generation of safe and efficient therapies for autoimmunity.
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Affiliation(s)
- Olga V Britanova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Kseniia R Lupyr
- Pirogov Russian National Research Medical University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Dmitry B Staroverov
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Dmitry V Somov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alesia Klimenko
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadejda A Shostak
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan V Zvyagin
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey V Stepanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ekaterina M Merzlyak
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- MiLaboratories Inc., Sunnyvale, CA, USA
| | | | - Evgeniy S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | | | | | | | - Denis A Fedorenko
- Department of Hematology and Chemotherapy, Pirogov National Medical and Surgical Center, Moscow, Russia
| | | | - Veronika I Skvortsova
- Pirogov Russian National Research Medical University, Moscow, Russia
- Federal Medical Biological Agency, Moscow, Russia
| | - Sergey Lukyanov
- Pirogov Russian National Research Medical University, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitry M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
- Abu Dhabi Stem Cell Center, Al Muntazah, United Arab Emirates.
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4
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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5
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Sorosina M, Santoro S, Ferrè L, Mascia E, Clarelli F, Giordano A, Cannizzaro M, Lucia M, Martinelli V, Filippi M, Esposito F. Risk HLA Variants Affect the T-Cell Repertoire in Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2023; 10:10/3/e200093. [PMID: 36792371 PMCID: PMC9931183 DOI: 10.1212/nxi.0000000000200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/14/2022] [Indexed: 02/17/2023]
Abstract
BACKGROUND AND OBJECTIVES The major histocompatibility complex (MHC) locus has a predominant role in the genetic predisposition to multiple sclerosis (MS), with 32 associations found to be involved. We aimed to investigate the impact of MHC MS-risk alleles on T-cell repertoire in patients with MS. METHODS We studied 161 untreated patients with relapsing-remitting MS for whom Class I and II human leukocyte antigen (HLA) alleles were inferred from whole-genome genotyping data, and T-cell receptor (TCR) CDR3 sequences were obtained through next-generation sequencing. T-cell repertoire features including diversity, public clones, and architecture were evaluated. RESULTS We identified 5 MS-risk loci associated with TCR diversity: HLA-DRB1*15:01 (7.65 × 10-3), rs9271366 (1.96 × 10-3), rs766848979 A (1.89 × 10-2), rs9277626 (2.95 × 10-2), and rs11751659 (1.92 × 10-2), with evidence of expanded clonotypes in carriers of risk alleles. Moreover, HLA-DRB1*15:01 (4.99 × 10-3), rs9271366 (6.54 × 10-3), rs1049079 C (4.37 × 10-2), AA DQΒ1 position -5 L (1.05 × 10-3), and AA DQΒ1 position 221 Q (9.39 × 10-4) showed an association with the CDR3 aminoacidic sequence architecture, suggesting an impact on the antigen recognition breadth as well. Evaluating the sharing of clones across MS-risk allele carrier individuals revealed the presence of highly shared clonotypes predicted to target viral antigens, including Epstein-Barr virus. DISCUSSION Our study supports the association between MHC-risk alleles and macrofeatures of the T-cell repertoire in the context of MS. Further studies are needed to understand the underlying molecular mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Federica Esposito
- From the Laboratory of Neurological Complex Disorders (M.S., S.S., L.F., E.M., F.C., A.G., M.C., F.E.), Division of Neuroscience, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute; Neurology and Neurorehabilitation Unit (L.F., A.G., M.C., M.L., V.M., M.F., F.E.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University (M.F.); Neurophysiology Unit (M.F.), IRCCS San Raffaele Scientific Institute; and Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE) (P.F.), IRCCS San Raffaele Scientific Institute, Milan, Italy.
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6
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 205] [Impact Index Per Article: 205.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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Bedri SK, Evertsson B, Khademi M, Al Nimer F, Olsson T, Hillert J, Glaser A. Copy number variations across the blood-brain barrier in multiple sclerosis. Ann Clin Transl Neurol 2022; 9:962-976. [PMID: 35560551 PMCID: PMC9268884 DOI: 10.1002/acn3.51573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022] Open
Abstract
Objective Multiple sclerosis (MS) is a neuroinflammatory disease where immune cells cross the blood–brain barrier (BBB) into the central nervous system (CNS). What predisposes these immune cells to cross the BBB is still unknown. Here, we examine the possibility that genomic rearrangements could predisposespecific immune cells in the peripheral blood to cross the BBB and form sub‐populations of cells involved in the inflammatory process in the CNS. Methods We compared copy number variations in paired peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) cells from MS patients. Thereafter, using next generation sequencing, we studied the T‐cell receptor beta (TRB) locus rearrangements and profiled the αβ T cell repertoire in peripheral CD4+ and CD8+ T cells and in the CSF. Results We identified deletions in the T‐cell receptor alpha/delta (TRA/D), gamma (TRG), and TRB loci in CSF cells compared to PBMCs. Further characterization revealed diversity of the TRB locus which was used to describe the character and clonal expansion of T cells in the CNS. T‐cell repertoire profiling from either side of the BBB concluded that the most frequent clones in the CSF samples are unique to an individual. Furthermore, we observed a difference in the proportion of expanded T‐cell clones when comparing samples from MS patients in relapse and remission with opposite trends in CSF and peripheral blood. Interpretation This study provides a characterization of the T cells in the CSF and might indicate a role of expanded clones in MS pathogenicity.
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Affiliation(s)
- Sahl Khalid Bedri
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Evertsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Mohsen Khademi
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Faiez Al Nimer
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Anna Glaser
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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8
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Amoriello R, Mariottini A, Ballerini C. Immunosenescence and Autoimmunity: Exploiting the T-Cell Receptor Repertoire to Investigate the Impact of Aging on Multiple Sclerosis. Front Immunol 2021; 12:799380. [PMID: 34925384 PMCID: PMC8673061 DOI: 10.3389/fimmu.2021.799380] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
T-cell receptor (TCR) repertoire diversity is a determining factor for the immune system capability in fighting infections and preventing autoimmunity. During life, the TCR repertoire diversity progressively declines as a physiological aging progress. The investigation of TCR repertoire dynamics over life represents a powerful tool unraveling the impact of immunosenescence in health and disease. Multiple Sclerosis (MS) is a demyelinating, inflammatory, T-cell mediated autoimmune disease of the Central Nervous System in which age is crucial: it is the most widespread neurological disease among young adults and, furthermore, patients age may impact on MS progression and treatments outcome. Crossing knowledge on the TCR repertoire dynamics over MS patients' life is fundamental to investigate disease mechanisms, and the advent of high- throughput sequencing (HTS) has significantly increased our knowledge on the topic. Here we report an overview of current literature about the impact of immunosenescence and age-related TCR dynamics variation in autoimmunity, including MS.
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Affiliation(s)
- Roberta Amoriello
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
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9
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Hayashi F, Isobe N, Cossu D, Yokoyama K, Sakoda A, Matsushita T, Hattori N, Kira JI. Elevated mycobacterium avium subsp. paratuberculosis (MAP) antibody titer in Japanese multiple sclerosis. J Neuroimmunol 2021; 360:577701. [PMID: 34507015 DOI: 10.1016/j.jneuroim.2021.577701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/07/2021] [Accepted: 08/22/2021] [Indexed: 11/30/2022]
Abstract
To investigate whether antibody production against mycobacterium avium subsp. paratuberculosis (MAP) is related to clinical characteristics of multiple sclerosis (MS) and human leukocyte antigen (HLA) alleles, IgG antibody against three MAP peptides and two human peptides homologous to MAP were measured in sera from 103 MS patients and 50 healthy controls (HCs). MS patients had higher IgG levels against MAP2694295-303 (MAP2694-IgG) than HCs, while the other antibodies were comparable. Multivariate analysis demonstrated that higher MAP2694-IgG titers were associated with higher EDSS scores, but not with HLA alleles or dairy product consumption. Immune response against MAP may worsen MS disability.
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Affiliation(s)
- Fumie Hayashi
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Davide Cossu
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan; Department of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, Italy
| | - Kazumasa Yokoyama
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Ayako Sakoda
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Neurology, Brain and Nerve Center, Fukuoka Central Hospital, International University of Health and Welfare, Fukuoka, Japan
| | - Takuya Matsushita
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan
| | - Jun-Ichi Kira
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Neurology, Brain and Nerve Center, Fukuoka Central Hospital, International University of Health and Welfare, Fukuoka, Japan; Translational Neuroscience Center, Graduate School of Medicine, School of Pharmacy at Fukuoka, International University of Health and Welfare, Fukuoka, Japan.
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10
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:e66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children’s Hospital and the Children’s Research Center, University of ZurichZurichSwitzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität DresdenDresdenGermany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3)ParisFrance
- AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi)ParisFrance
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of MedicineAtlantaUnited States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Davide Bagnara
- University of Genoa, Department of Experimental MedicineGenoaItaly
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashvilleUnited States
- Department of Pediatrics, Vanderbilt University Medical CenterNashvilleUnited States
| | - Jacob S Sherkow
- College of Law, University of IllinoisChampaignUnited States
- Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of LawCopenhagenDenmark
- Carl R. Woese Institute for Genomic Biology, University of IllinoisUrbana, IllinoisUnited States
| | - Aimee S Payne
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
- Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of MontpellierMontpellierFrance
- Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
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